Genomic Characterization of Multidrug-Resistant Extended Spectrum β-Lactamase-Producing Klebsiella pneumoniae from Clinical Samples of a Tertiary Hospital in South Kivu Province, Eastern Democratic Republic of Congo
Abstract
:1. Introduction
2. Materials and Methods
2.1. Ethical Clearance
2.2. Bacterial Strains
2.3. Antimicrobial Susceptibility Testing
2.4. Bacterial DNA Extraction
2.5. Library Preparation and Next Generation Sequencing
2.6. Genome Assembly, Annotation, and Alignment
3. Results
3.1. Bacterial Strains
3.2. Antimicrobial Susceptibility Testing
3.3. Phylogenomic Analysis
3.4. Genetic Determinants of Virulence
3.4.1. Detection of Virulence Factors Genes
3.4.2. Replicon Typing
3.4.3. Identification of the Capsule Type
3.4.4. Detection of AMR Genes
3.4.5. Detection of AMR Point Mutations
4. Discussion
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Isolate | Tissue | ST | AMP | AMX | AMC | FEP | CTX | CAZ | CRO | IPM | MERO | CIP | AKN | GENT | TET | COL | NITRO |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTMA-1678 | Bloodstream | 340 | >256 | >256 | >256 | 48 | >256 | >256 | >32 | 0.094 | 0.75 | >32 | 12 | 96 | >256 | 0.25 | >512 |
CTMA-1674 | Bloodstream | 340 | >256 | >256 | >256 | 64 | >256 | >256 | >32 | 0.094 | 0.094 | >32 | 6 | >256 | >256 | 0.25 | >512 |
CTMA-1676 | Bloodstream | 340 | >256 | >256 | >256 | 64 | >256 | >256 | >32 | 0.094 | 0.047 | >32 | 8 | 64 | >256 | 0.25 | >512 |
CTMA-1653 | Bloodstream | 340 | >256 | >256 | >256 | 32 | >256 | >256 | >32 | 0.5 | 0.47 | >32 | 8 | 64 | >256 | 0.25 | >512 |
CTMA-1690 | UTI | 340 | >256 | >256 | >256 | 64 | >256 | 192 | >32 | 0.19 | 0.094 | >32 | 8 | 128 | >256 | <0.25 | >512 |
CTMA-1668 | UTI | 15 | >256 | >256 | >256 | 48 | >256 | >256 | >32 | 0.25 | 0.032 | >32 | 6 | 96 | >256 | 0.25 | 48 |
CTMA-1660 | UTI | 37 | >256 | >256 | 16 | 0.25 | 12 | 12 | >32 | 0.125 | 0.023 | 1 | 24 | >256 | >256 | <0.25 | 3 |
CTMA-1656 | UTI | 37 | >256 | >256 | >256 | 0.75 | 24 | 24 | >32 | 0.19 | 0.23 | 1 | 32 | >256 | >256 | 0.25 | 6 |
CTMA-1654 | UTI | 309 | >256 | >256 | >256 | 12 | >256 | >256 | >32 | 0.125 | 0.032 | >32 | 24 | >256 | >256 | 0.25 | 64 |
CTMA-1689 | UTI | 16 | >256 | >256 | >256 | 48 | >256 | >256 | >32 | 0.25 | 0.002 | >32 | 8 | 96 | >256 | 0.25 | >512 |
CTMA-1682 | UTI | 2094 | >256 | >256 | >256 | 64 | >256 | >256 | >32 | 0.023 | 0.125 | >32 | 12 | 48 | 4 | 0.5 | 32 |
CTMA-1677 | Bloodstream | 1777 | >256 | >256 | >256 | 12 | 64 | 16 | >32 | 0.094 | 0.064 | 1.5 | 3 | 96 | >256 | 0.25 | >512 |
CTMA-1673 | Bloodstream | 1777 | >256 | >256 | 12 | 12 | >256 | >256 | >32 | 0.25 | 0.047 | 1.5 | 3 | 96 | >256 | 0.25 | 128 |
CTMA-1665 | Peritoneal fluid | 502 | >256 | >256 | >256 | 24 | >256 | >256 | >32 | 0.002 | 0.23 | 4 | 24 | 128 | >256 | <0.25 | 12 |
CTMA-1680 | Bloodstream | 39 | >256 | >256 | >256 | 24 | 96 | >256 | >32 | 0.125 | 0.032 | 3 | 48 | >256 | >256 | 0.25 | 96 |
CTMA-1679 | Bloodstream | 39 | >256 | >256 | >256 | 24 | >256 | >256 | >32 | 0.125 | 0.064 | 2 | 48 | >256 | >256 | 0.25 | 32 |
CTMA-1681 | Bloodstream | 39 | >256 | >256 | >256 | 32 | >256 | 32 | >32 | 0.125 | 0.032 | 2 | 64 | >256 | >256 | 0.5 | 96 |
CTMA-1655 | UTI | 39 | >256 | >256 | >256 | 32 | >256 | >256 | >32 | 0.19 | 0.32 | 2 | 24 | >256 | >256 | 0.25 | 6 |
CTMA-1664 | UTI | 967 | >256 | >256 | 8 | 8 | >256 | 24 | >32 | 0.064 | 0.47 | 1.5 | 8 | 24 | >256 | 0.25 | 64 |
CTMA-1659 | UTI | 337 | >256 | >256 | 8 | 24 | >256 | 16 | >32 | 0.125 | 0.05 | 0.75 | 2 | 0.75 | >256 | 0.25 | 24 |
CTMA-1661 | Soft tissue | 48 | >256 | >256 | >256 | 16 | >256 | >256 | >32 | 0.094 | 0.023 | 6 | 6 | 32 | >256 | <0.25 | 128 |
CTMA-1666 | Bloodstream | 48 | >256 | >256 | 64 | 8 | >256 | >256 | >32 | 0.023 | 0.125 | 1.5 | 8 | 24 | 64 | <0.25 | 96 |
CTMA-1672 | Bloodstream | 48 | >256 | >256 | 1.5 | 16 | >256 | >256 | >32 | 0.19 | 0.047 | >32 | 16 | 96 | >256 | 0.25 | >512 |
CTMA-1684 | Bloodstream | 48 | >256 | >256 | >256 | 16 | >256 | >256 | >32 | 0.094 | 0.047 | 8 | 12 | 32 | 16 | 0.5 | 128 |
CTMA-1650 | Bloodstream | 48 | >256 | >256 | >256 | 16 | >256 | >256 | >32 | 0.094 | 0.023 | >32 | 16 | 96 | >256 | 0.25 | >512 |
CTMA-1662 | Soft tissue | 48 | >256 | >256 | 64 | 24 | >256 | >256 | >32 | 0.094 | 0.023 | 6 | 6 | 32 | >256 | <0.25 | 128 |
CTMA-1667 | Bloodstream | 874 | >256 | >256 | >256 | 1.5 | >256 | >256 | >32 | 0.047 | 0.094 | 0.5 | 38 | 0.094 | >256 | 0.25 | 16 |
CTMA-1663 | Bloodstream | 874 | >256 | >256 | 48 | 24 | >256 | >256 | >32 | 0.5 | 0.047 | >32 | 8 | 96 | >256 | 0.25 | 192 |
CTMA-1683 | Bloodstream | 607 | >256 | >256 | >256 | 16 | >256 | >256 | >32 | 0.256 | 0.125 | 2 | 4 | 128 | >256 | 0.25 | >512 |
CTMA-1687 | UTI | 607 | >256 | >256 | >256 | >256 | >256 | >256 | >32 | 0.094 | 0.064 | 1.000 | 3 | >256 | >256 | 0.5 | >512 |
CTMA-1686 | UTI | 607 | >256 | >256 | >256 | >256 | >256 | >256 | >32 | 0.19 | 0.023 | 0.094 | 6 | 192 | 1.5 | 0.5 | >512 |
CTMA-1671 | Bloodstream | 607 | >256 | >256 | >256 | 1.5 | >256 | >256 | >32 | 0.094 | 0.047 | >32.000 | 12 | 128 | >256 | 0.25 | >512 |
CTMA-1675 | Bloodstream | 607 | >256 | >256 | >256 | 48 | >256 | >256 | >32 | 0.125 | 0.047 | 0.125 | 4 | >256 | >256 | 0.25 | 192 |
CTMA-1652 | UTI | 607 | >256 | >256 | >256 | >256 | >256 | >256 | >32 | 0.125 | 0.47 | 0.125 | 4 | >256 | >256 | 0.25 | >512 |
CTMA-1685 | UTI | 14 | >256 | >256 | >256 | 6 | >256 | >256 | >32 | 0.19 | 0.023 | 1.5 | 6 | 96 | 128 | 0.5 | >512 |
CTMA-1657 | UTI | 15 | >256 | >256 | >256 | 16 | >256 | >256 | >32 | 0.125 | 0.06 | >32 | 8 | 64 | >256 | 0.25 | 64 |
CTMA-1688 | Bloodstream | 11 | >256 | >256 | >256 | 48 | >256 | >256 | >32 | 0.256 | 0.023 | 1.500 | 6 | 64 | 2 | 0.25 | 48 |
Antibiotics | Resistance (R) n = 37 (%) | Susceptible (S) n = 37 (%) | Area of Technical Uncertainty (ATU) n = 37 (%) |
---|---|---|---|
Ampicillin | 37 (100) | 0 (0) | 0 (0) |
Amoxicillin | 37 (100) | 0 (0) | 0 (0) |
Amoxicillin-clavulanate | 35 (94.6) | 2 (5.4) | 0 (0) |
Cefepime | 34 (91.9) | 3 (8.1) | 0 (0) |
Cefotaxime | 37 (100) | 0 (0) | 0 (0) |
Ceftazidime | 37 (100) | 0 (0) | 0 (0) |
Ceftriaxone | 37 (100) | 0 (0) | 0 (0) |
Imipenem | 0 (0) | 37 (100) | 0 (0) |
Meropenem | 0 (0) | 37 (100) | 0 (0) |
Ciprofloxacin | 35 (94.6) | 1 (2.7) | 1 (2.7) |
Amikacin | 15 (40.5) | 22 (59.5) | 0 (0) |
Gentamicin | 35 (94.6) | 2 (5.4) | 0 (0) |
Tetracycline | 34 (91.9) | 3 (8.1) | 0 (0) |
Colistin | 0 (0) | 37 (100) | 0 (0) |
Nitrofurantoin | 24 (64.9) | 13 (35.1) | 0 (0) |
Year of Isolation | Strain | Origin | ST | Replicon ST | K_Type | O Type | Yersiniabactin | (Hyper) Virulence Genes | Virulence Score |
---|---|---|---|---|---|---|---|---|---|
2014 | CTMA_1678 | Bloodstream | ST340 | F1:A−:B− | unknown (KL107) | unknown (O4) | ybt 9; ICEKp3 (truncated) | - | 1 |
2014 | CTMA_1674 | Bloodstream | ST340 | F1:A13:B− | unknown (K15) | O4 | ybt 9; ICEKp3 (truncated) | - | 1 |
2014 | CTMA_1676 | Bloodstream | ST340 | F1:A13:B− | unknown (K15) | O4 | ybt 9; ICEKp3 (truncated) | - | 1 |
2014 | CTMA_1653 | Bloodstream | ST340 | F1:A13:B− | unknown (KL107) | unknown (O4) | ybt 9; ICEKp3 (truncated) | - | 1 |
2013 | CTMA_1690 | UTI | ST340 | F−:A13:B− | unknown (K15) | O4 | ybt 14; ICEKp5 | - | 1 |
2013 | CTMA_1688 | UTI | ST11 | F13:A13:B− | unknown (KL105) | O2afg | ybt 9; ICEKp3 | - | 1 |
2014 | CTMA_1660 | UTI | ST37 | F−:A13:B− | K14 | O3b | ybt 15; ICEKp11 | - | 1 |
2014 | CTMA_1656 | UTI | ST37 | F−:A13:B− | K14 | O3b | ybt 15; ICEKp11 | - | 1 |
2014 | CTMA_1654 | UTI | ST309 | ND | unknown (K42) | unknown (O4) | - | - | 0 |
2013 | CTMA_1689 | UTI | ST16 | F12:A26:B− | unknown (K51) | O3b | ybt 9; ICEKp3 | - | 1 |
2016 | CTMA_1682 | UTI | ST2094 | F−:A13:B− | unknown (KL107) | unknown (OL101) | - | - | 0 |
2014 | CTMA_1677 | Bloodstream | ST1777 | F13:A13:B− | unknown (KL111) | O3b | - | - | 0 |
2014 | CTMA_1673 | Bloodstream | ST1777 | F13:A13:B− | unknown (KL111) | O3b | - | - | 0 |
2015 | CTMA_1665 | Soft tissue | ST502 | F13:A−:B− | unknown (K15) | unknown (O4) | - | - | 0 |
2015 | CTMA_1680 | Bloodstream | ST39 | F2:A13:B− | unknown (K2) | O2a | ybt 16; ICEKp12 | - | 1 |
2015 | CTMA_1679 | Bloodstream | ST39 | F2:A13:B− | unknown (K2) | O1 | ybt 16; ICEKp12 | - | 1 |
2015 | CTMA_1681 | Bloodstream | ST39 | F2:A13:B− | unknown (K2) | O1 | ybt 16; ICEKp12 | - | 1 |
2015 | CTMA_1655 | UTI | ST39 | F2:A13:B− | K2 | O1 | ybt 16; ICEKp12 | - | 1 |
2014 | CTMA_1664 | UTI | ST967 | F2:A−:B− | unknown (K18) | O2afg | - | - | 0 |
2014 | CTMA_1659 | UTI | ST337 | ND | unknown (KL109) | O2afg | - | - | 0 |
2015 | CTMA_1661 | Peritoneal fluid | ST48 | F13:A−:B− | unknown (K62) | O1 | ybt 14; ICEKp5 | - | 1 |
2014 | CTMA_1666 | Bloodstream | ST48 | F13:A−:B− | unknown (K62) | O2a | ybt 14; ICEKp5 | - | 1 |
2015 | CTMA_1672 | Bloodstream | ST48 | F13:A−:B− | unknown (K62) | unknown (O2a) | ybt 14; ICEKp5 | - | 1 |
2016 | CTMA_1684 | Bloodstream | ST48 | F13:A−:B− | unknown (K62) | O1 | ybt 14; ICEKp5 | - | 1 |
2014 | CTMA_1650 | Bloodstream | ST48 | F13:A−:B− | K62 | O1 | ybt 14; ICEKp5 | - | 1 |
2015 | CTMA_1662 | Peritoneal fluid | ST48 | F13:A−:B− | unknown (K62) | O1 | ybt 14; ICEKp5 | - | 1 |
2014 | CTMA_1667 | Bloodstream | ST874 | ND | unknown (K45) | O1 | ybt 14; ICEKp12 | - | 1 |
2015 | CTMA_1663 | Bloodstream | ST874 | ND | unknown (K45) | unknown (O1) | ybt 14; ICEKp12 | - | 1 |
2017 | CTMA_1683 | Bloodstream | ST607 | F13:A13:B− | unknown (K25) | O1 | ybt 14; ICEKp5 | - | 1 |
2014 | CTMA_1687 | UTI | ST607 | F13:A13:B− | unknown (K25) | O1 | - | - | 0 |
2017 | CTMA_1686 | UTI | ST607 | F13:A13:B− | unknown (K25) | O1 | ybt 14; ICEKp5 | - | 1 |
2014 | CTMA_1671 | Bloodstream | ST607 | F13:A13:B− | unknown (K25) | O2a | ybt 14; ICEKp5 | - | 1 |
2017 | CTMA_1675 | Bloodstream | ST607 | F13:A13:B− | unknown (K25) | O1 | ybt 14; ICEKp5 | - | 1 |
2015 | CTMA_1652 | UTI | ST607 | F13:A13:B− | unknown (K25) | O2a | ybt 14; ICEKp5 | - | 1 |
2013 | CTMA_1685 | UTI | ST14 | F9:A−:B− | K2 | O1 | - | 0 | |
2014 | CTMA_1657 | UTI | ST15 | F8:A13:B− | unknown (KL112) | O1 | - | - | 0 |
2013 | CTMA_1668 | Bloodstream | ST15 | F−:A13:B− | unknown (K48) | O2a | - | - | 0 |
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Irenge, L.M.; Ambroise, J.; Bearzatto, B.; Durant, J.-F.; Bonjean, M.; Gala, J.-L. Genomic Characterization of Multidrug-Resistant Extended Spectrum β-Lactamase-Producing Klebsiella pneumoniae from Clinical Samples of a Tertiary Hospital in South Kivu Province, Eastern Democratic Republic of Congo. Microorganisms 2023, 11, 525. https://doi.org/10.3390/microorganisms11020525
Irenge LM, Ambroise J, Bearzatto B, Durant J-F, Bonjean M, Gala J-L. Genomic Characterization of Multidrug-Resistant Extended Spectrum β-Lactamase-Producing Klebsiella pneumoniae from Clinical Samples of a Tertiary Hospital in South Kivu Province, Eastern Democratic Republic of Congo. Microorganisms. 2023; 11(2):525. https://doi.org/10.3390/microorganisms11020525
Chicago/Turabian StyleIrenge, Leonid M., Jérôme Ambroise, Bertrand Bearzatto, Jean-François Durant, Maxime Bonjean, and Jean-Luc Gala. 2023. "Genomic Characterization of Multidrug-Resistant Extended Spectrum β-Lactamase-Producing Klebsiella pneumoniae from Clinical Samples of a Tertiary Hospital in South Kivu Province, Eastern Democratic Republic of Congo" Microorganisms 11, no. 2: 525. https://doi.org/10.3390/microorganisms11020525
APA StyleIrenge, L. M., Ambroise, J., Bearzatto, B., Durant, J.-F., Bonjean, M., & Gala, J.-L. (2023). Genomic Characterization of Multidrug-Resistant Extended Spectrum β-Lactamase-Producing Klebsiella pneumoniae from Clinical Samples of a Tertiary Hospital in South Kivu Province, Eastern Democratic Republic of Congo. Microorganisms, 11(2), 525. https://doi.org/10.3390/microorganisms11020525